DNA Barcoding and Emerging eDNA Applications for Indonesian Gobiidae Biodiversity Assessment: A Systematic Literature Review

Abstract

Background: Indonesian Gobiidae comprise ecologically important freshwater and amphidromous fishes, but accurate biodiversity assessment is often constrained by morphological similarity, poorly developed diagnostic characters in larval stages, and incomplete taxonomic information. DNA barcoding can improve species-level identification and reveal cryptic diversity, whereas environmental DNA (eDNA) offers an emerging, non-invasive approach for biodiversity monitoring. However, evidence on the application of these molecular tools to Indonesian Gobiidae remains fragmented. Aims: To systematically evaluate the application of DNA barcoding and emerging environmental DNA (eDNA) approaches in assessing the biodiversity of Indonesian Gobiidae, with particular emphasis on species identification, cryptic diversity, biogeographic patterns, and amphidromous larval assemblages such as nike fish. Study Design: A Scopus-based systematic literature review with qualitative synthesis. Place and Duration of Study: The literature search was conducted using the Scopus database on 1 May 2026 and covered studies published between 2016 and 2026. Methodology: The Scopus database was searched using combinations of keywords related to Gobiidae, gobiid fishes, amphidromous taxa, Indonesian biogeographic regions, DNA barcoding, cytochrome c oxidase subunit I (COI), eDNA, biodiversity assessment, and species distribution. The retrieved records were screened for relevance to the molecular identification and biodiversity assessment of Indonesian Gobiidae and related freshwater and amphidromous fishes. Of the 319 records initially retrieved, 29 studies that met the eligibility criteria were included in the qualitative synthesis. Results: Of the 319 records identified, 29 studies (9.1%) published between 2016 and 2026 were included in the review. The evidence indicates that COI-based DNA barcoding improves the accuracy of species identification, contributes to the development of molecular reference libraries, and reveals cryptic diversity and biogeographic differentiation among Indonesian freshwater and amphidromous fishes. Molecular approaches are particularly important for identifying nike fish assemblages because larval gobies possess poorly developed and overlapping morphological characters that limit reliable species-level identification. In comparison with conventional DNA barcoding, the application of eDNA to Indonesian Gobiidae remains limited, although it offers a promising non-invasive tool for monitoring gobiid diversity across freshwater, estuarine, and coastal-connected habitats. The major limitations identified were incomplete barcode reference libraries, uneven geographic coverage, limited standardisation of eDNA protocols, and insufficient long-term monitoring of amphidromous recruitment. Conclusion: DNA barcoding provides a valuable approach for improving the identification and biodiversity assessment of Indonesian Gobiidae, particularly for morphologically indistinguishable larval assemblages. The integration of DNA barcoding, eDNA, conventional ecological surveys, and local fisheries knowledge could support more comprehensive biodiversity monitoring and conservation planning. However, broader geographic sampling, more complete and validated reference libraries, standardised eDNA protocols, and long-term monitoring are required to strengthen the reliability and applicability of these molecular approaches.